On 3/4/13 11:25 AM, Kavyashree M wrote:
Dear users,
I used the following tool for finding the contacts
g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn a.ndx
-num a.xvg
From the index file, the number of contacts of each atom was extracted.
This and the
xvg output was compared with another simulation.
It was found that the number of contacts was more in 2nd simulation
compared to
the first. But When I compared xvg file it was showing the opposite
behaviour.
These statements don't make any sense. How did you determine that the number of
contacts in simulation 2 was greater than simulation 1, but then the .xvg files
showed the opposite? The number of contacts come from the .xvg files? Perhaps
you simply swapped your files during analysis.
The contacts was also calculated using g_mdmat for the same cutoff and it
was agreeing
with the numbers I got from in index output of g_hbond.
Why is this difference in index and xvg output?
An index group is a list of atom numbers. The .xvg output is whatever you tell
it to be, in this case, the number of contacts within the group selected.
-Justin
Also the xvg file looks like -
s0 legend "Contacts"
@ s1 legend "Pairs within 0.4 nm"
4000 7496 0
4002 7513 0
4004 7605 0
4006 7531 0
4008 7573 0
4010 7546 0
4012 7544 0
4014 7526 0
4016 7530 0
4018 7496 0
4020 7526 0
..
Thank you
kavya
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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